Genetic Variant MTNR1B:c.*16A>G (chr11-92984997-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000528076.1(MTNR1B):c.*16A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.572 in 451,308 control chromosomes in the GnomAD database, including 75,820 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.56 ( 23976 hom., cov: 33)

Exomes 𝑓: 0.58 ( 51844 hom. )

Consequence

MTNR1B
ENST00000528076.1 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.142

Publications

12 publications found

Variant links:

Genes affected

MTNR1B (HGNC:7464): (melatonin receptor 1B) This gene encodes one of two high affinity forms of a receptor for melatonin, the primary hormone secreted by the pineal gland. This gene product is an integral membrane protein that is a G-protein coupled, 7-transmembrane receptor. It is found primarily in the retina and brain although this detection requires RT-PCR. It is thought to participate in light-dependent functions in the retina and may be involved in the neurobiological effects of melatonin. [provided by RefSeq, Jul 2008]

MTNR1B links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.76).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.676 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MTNR1B	XM_011542839.3 link	c.*602A>G		downstream_gene_variant			XP_011541141.1	P49286
MTNR1B	XM_017017777.2 link	c.*602A>G		downstream_gene_variant			XP_016873266.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MTNR1B	ENST00000528076.1 link	c.*16A>G		3_prime_UTR_variant	Exon 2 of 2	3		ENSP00000433573.1		H0YDG4

Frequencies

GnomAD3 genomes

AF:

0.557

AC:

84639

AN:

151924

Hom.:

23944

Cov.:

show subpopulations

Gnomad AFR

AF:

0.558

Gnomad AMI

AF:

0.681

Gnomad AMR

AF:

0.656

Gnomad ASJ

AF:

0.439

Gnomad EAS

AF:

0.695

Gnomad SAS

AF:

0.684

Gnomad FIN

AF:

0.575

Gnomad MID

AF:

0.583

Gnomad NFE

AF:

0.516

Gnomad OTH

AF:

0.543

GnomAD2 exomes

AF:

0.607

AC:

75236

AN:

124000

AF XY:

0.604

show subpopulations

Gnomad AFR exome

AF:

0.554

Gnomad AMR exome

AF:

0.750

Gnomad ASJ exome

AF:

0.436

Gnomad EAS exome

AF:

0.684

Gnomad FIN exome

AF:

0.587

Gnomad NFE exome

AF:

0.518

Gnomad OTH exome

AF:

0.566

GnomAD4 exome

AF:

0.579

AC:

173359

AN:

299268

Hom.:

51844

Cov.:

AF XY:

0.587

AC XY:

100100

AN XY:

170548

show subpopulations

African (AFR)

AF:

0.557

AC:

4717

AN:

8476

American (AMR)

AF:

0.748

AC:

20154

AN:

26928

Ashkenazi Jewish (ASJ)

AF:

0.433

AC:

4487

AN:

10370

East Asian (EAS)

AF:

0.685

AC:

6294

AN:

9186

South Asian (SAS)

AF:

0.681

AC:

40016

AN:

58738

European-Finnish (FIN)

AF:

0.580

AC:

7068

AN:

12182

Middle Eastern (MID)

AF:

0.560

AC:

1532

AN:

2738

European-Non Finnish (NFE)

AF:

0.519

AC:

81316

AN:

156640

Other (OTH)

AF:

0.555

AC:

7775

AN:

14010

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

3483

6967

10450

13934

17417

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

556

1112

1668

2224

2780

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.557

AC:

84733

AN:

152040

Hom.:

23976

Cov.:

AF XY:

0.565

AC XY:

41996

AN XY:

74300

show subpopulations

African (AFR)

AF:

0.559

AC:

23172

AN:

41470

American (AMR)

AF:

0.657

AC:

10042

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.439

AC:

1525

AN:

3472

East Asian (EAS)

AF:

0.695

AC:

3579

AN:

5146

South Asian (SAS)

AF:

0.684

AC:

3299

AN:

4820

European-Finnish (FIN)

AF:

0.575

AC:

6080

AN:

10566

Middle Eastern (MID)

AF:

0.586

AC:

171

AN:

292

European-Non Finnish (NFE)

AF:

0.516

AC:

35101

AN:

67974

Other (OTH)

AF:

0.543

AC:

1143

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1912

3824

5735

7647

9559

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

726

1452

2178

2904

3630

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.526

Hom.:

4742

Bravo

AF:

0.565

Asia WGS

AF:

0.646

AC:

2245

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.76

CADD

Benign

7.6

(source)

DANN

Benign

0.88

PhyloP100

-0.14

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over